The design of the experiments (table with parameters) can be found here. But here is a brief description.
| PS | N_GENES_INITIAL | BITING_RATE_MEAN | N_LOCI | N_ALLELES_INITIAL |
|---|---|---|---|---|
| 01 | 120 | 0.1 | 2 | 12 |
| 02 | 1200 | 0.2 | 2 | 120 |
| 03 | 12000 | 0.5 | 2 | 1200 |
I kept daily biting rates fixed to 1.
In the complete neutrality, the number of circulating strains seems just too much. This is orders of magnitude more than the selection.
## [1] "PS: 01 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 02 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 03 | Scenario: S | exp: 001 | run: 1"
## [1] "PS: 01 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 02 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 03 | Scenario: N | exp: 001 | run: 1"
## [1] "PS: 01 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 02 | Scenario: G | exp: 001 | run: 1"
## [1] "PS: 03 | Scenario: G | exp: 001 | run: 1"
The EIR for selection seems too low? For neutrality it is an order of magnitude more.
Notice the order of magnitude difference in the number of repertoires
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
## [1] "Scenario: S | exp: 001 | run: 1"
## [1] "Scenario: N | exp: 001 | run: 1"
## [1] "Scenario: G | exp: 001 | run: 1"
For now cannot plot the high diversity because there are just too many edges (computer crashes)
This will be influenced by cutoff. For now I am using the cutoffs I used in the previous version: 0.25 (low), 0.7 (medium), 0.9 (high).
## [1] "04 | S | 001 | 1 | 0.25"
## [1] "05 | S | 001 | 1 | 0.7"
## [1] "06 | S | 001 | 1 | 0.9"
## [1] "04 | N | 001 | 1 | 0.25"
## [1] "05 | N | 001 | 1 | 0.7"
## [1] "06 | N | 001 | 1 | 0.9"
## [1] "04 | G | 001 | 1 | 0.25"
## [1] "05 | G | 001 | 1 | 0.7"
## [1] "06 | G | 001 | 1 | 0.9"
Persistence of repertories is after removing duplicates. Gray is repertoires.
Persistence of repertories is after removing duplicates. Gray is repertoires.